A picture found among the belongings of a victim, held by a forensic anthropologist in the general prosecutor’s laboratory in Medellin, above. Photograph: Raul Arboleda/AFP/Getty Images

A tangle of jungle covers the banks of the muddy stream that cuts through the San Jorge ranch. Lianas hang down from overhead and woody vines grow in knots on the sandy ground. Somewhere beneath the heavy soil lie dozens of bodies – victims of Colombia's four-decade civil war who were killed by rightwing paramilitaries and buried where they fell.

Among the dead are two oil workers suspected of collaborating with leftwing guerrillas. There are also at least half a dozen paramilitary fighters killed in a series of purges within the group. And there are Luz Neira Achagua and her lover, Yovany Quevedo. She was killed after someone accused her of being a rebel; he was killed for his motorbike, which the local paramilitary commander had taken a fancy to.

A former paramilitary fighter who goes by the alias Aguila (Eagle) was one of a group of men who kidnapped Achagua and Quevedo from their home in the town of Aguazul in Casanare province in the eastern lowlands. He told investigators they had been held at the ranch for days before being shot. Quevedo was buried just beside the river, Achagua in a thicket about 20 metres away.

On a recent, steamy day, Aguila guided a team of forensic scientists and prosecutors in search of their remains. Quevedo's sister Lyda and Achagua's daughter Jeiny looked on as Aguila tried to get his bearings.

Across Colombia, jailed paramilitary fighters such as Aguila are leaving their cells and heading back to the countryside they once ruled. But now they are revisiting the scenes of their crimes chained to prison guards and escorted by dozens of heavily armed police and soldiers.

"This is the last thing I thought we would be doing," said Aguila as he broke the earth with a shovel, helping the team to dig where he thought Quevedo was buried. "We just buried them as quickly as we could and forgot about it."

Now, however, it is in the best interests of the former paramilitaries to remember, as it is their ticket to shorter prison sentences and other benefits under the so-called justice and peace law, which governs the demobilisation of some 27,000 militiamen between 2003 and 2005. To earn the legal benefits, the fighters must confess their crimes, which includes helping prosecutors to locate the bodies of the victims they helped to make disappear.

More than 31,200 Colombians were disappeared by the paramilitaries in the decade and a half when they controlled much of the country, fighting leftist guerrillas and anyone suspected of working with them, and in the process taking swaths of fertile farmland from helpless peasants. Most of the disappeared are presumed dead.

Marta Gutierrez's 15-year-old son, John Mario Giraldo, disappeared in 1988 along with 17 miners in San Rafael, in the western province of Antioquia. She recently witnessed the exhumation of what she believes are his remains, but will have to wait for up to a year before forensic scientists can confirm they are his. "Even if it's two or three bones they can return to me, it will be a relief," she said. Then, at least, she can stop imagining that he might one day show up alive.

What she wants, she says, is justice: "Someone has to pay."

But if anyone is found guilty of John Mario's death, the price they pay will not be high. Under the justice and peace law, paramilitaries who were demobilised before 2005, and who confess all their crimes and offer reparations to their victims, can receive a maximum prison sentence of only eight years.

Five years after the law was enacted, after former militia chiefs have confessed to thousands of murders, massacres and disappearances, the first two convictions were handed down just at the end of June. Most of the senior paramilitary chiefs were extradited to the United States and convicted on drug charges. Meanwhile, many of those who were demobilised have formed new militia groups.

Critics say the lack of sentences for some of the most brutal criminals in Colombia's conflict proves the transitional justice experiment a complete failure. Yet the outgoing government of Alvaro Uribe wanted Congress to extend the law to include crimes committed after the original cut-off date. The bill stalled and it is unclear whether the president-elect, Juan Manuel Santos, once Uribe's defence minister, will reintroduce the measure when he takes power on 7 August.

Michael Reed, director of the Colombian office of the International Centre for Transitional Justice, believes the proposal is "inconvenient, misguided and dangerous". He said: "Before expanding the scope, it would be good to show some results and to perfect the functioning of the current justice and peace law."

So far, the only success in the process has been the discovery of thousands of clandestine graves throughout the country. Since efforts to dig up the missing began in 2006, 3,269 bodies have been found in 2,694 graves, some deep, some shallow, nearly always unmarked. Often the bodies were quartered and beheaded, to save the gravediggers the work of making a big hole. An untold number were thrown into rivers. Some of the more sophisticated paramilitary fronts had crematoriums.

The search for the bodies has become routine, with special prosecutors arranging for teams to scour the countryside for two weeks every month, mobilising special police squads, army units and prison guards. "This may cost all the money in the world, but being able to give the remains of someone to their family is priceless," said Nelson Cárdenas, the prosecutor in charge of the exhumation mission in Casanare province.

After her brother's death, Lyda Quevedo founded an organisation for the victims of paramilitary violence which has helped other families to find the remains of their loved ones. At the San Jorge ranch, she came face to face with the man responsible for his death. "I talk to them because they are the ones who know the truth," she said. "It's the only way I'll ever know the truth."

As the forensic team worked, Aguila approached Quevedo and asked for forgiveness. "In the war it was as if we couldn't feel anything. We were given orders, and we followed," he said. She looked in his eyes and nodded. "I just want to find my brother," she said.

The forensic team dug all day in four spots pointed out by Aguila, looking for evidence that the earth had been moved, or any indication of decomposition.

But after hours of surveying, digging, searching and pacing, the team gave up. The inmates and guards, soldiers, forensic experts, prosecutor and victims marched back along the riverside and piled into waiting trucks. Aguila was clearly frustrated that the graves had not been found. Quevedo was shattered.

History of violence

Colombia's conflict started in the 1960s as a battle between the state and peasant-backed guerrillas inspired by Cuba-style socialism. In the 1980s big landowners and drug dealers created paramilitary militias to help fend off extortion and kidnapping by the rebels. The paramilitaries morphed into a private army, the United Self-Defence Forces of Colombia (AUC). Like their guerrilla foes, the "paras" became directly involved in extortion and the drugs trade, and forced thousands of peasants from valuable land, generating vast wealth. The state started demobilising paramilitaries in 2004, but many have reformed under new names such as the Black Eagles and operate as a mafia, smuggling, extorting and assassinating. The guerrillas, though in decline, still control swaths of jungle. Of more than 3m who have fled their homes, few have returned.

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